What is QIIME?

QIIME 2 has succeeded QIIME 1 as of January 1, 2018. QIIME 1 is no longer supported at this time, as development and support effort for QIIME is now focused entirely on QIIME 2. For more information, see our blog post: QIIME 2 has succeeded QIIME 1.

QIIME 1 users should transition from QIIME 1 to QIIME 2. If you're new to QIIME, you should start by learning QIIME 2, not QIIME 1.

QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication quality graphics and statistics.
This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, and phylogenetic reconstruction, and diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.

Running: Once you've installed QIIME, move on to the QIIME Tutorials. The Illumina overview tutorial or the 454 overview tutorial are good first analyses to run. In each of these tutorials you'll download a small data set and work through a series of commands that will introduce you to some of QIIME's commonly used features and analyses.